Contacts of the helix formed by residues 585 - 593 (chain A) in PDB entry 5QSY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 585 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A ASP* 3.9 6.8 - - - +
523A SER* 5.0 0.5 + - - -
582A TYR* 3.0 14.1 + - + +
584A ALA* 1.3 75.9 - - - +
586A ALA* 1.3 63.8 + - - +
587A GLU* 3.3 16.4 + - - +
588A LYS* 2.6 59.6 + - + +
589A VAL* 3.0 26.5 + - - +
627A HIS* 4.3 0.2 - - - -
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Residues in contact with ALA 586 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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584A ALA 3.2 7.8 + - - +
585A ASP* 1.3 72.1 + - - +
587A GLU* 1.3 72.2 + - - +
589A VAL* 4.0 1.7 - - - -
590A ALA* 3.1 20.6 + - - +
627A HIS* 3.9 6.7 - - - +
629A GLU* 3.6 38.1 - - + +
631A ASP* 5.8 0.3 - - - +
632A VAL* 3.4 24.3 - - + +
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Residues in contact with GLU 587 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A SER* 5.7 3.8 - - - +
585A ASP* 3.3 12.2 - - - +
586A ALA* 1.3 84.8 + - - +
588A LYS* 1.3 63.8 + - + +
590A ALA* 3.4 7.3 + - - +
591A ASN* 3.2 22.9 + - - +
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Residues in contact with LYS 588 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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519A ASP* 3.3 25.9 + - - +
522A GLU* 3.9 14.1 + - - +
523A SER* 3.1 45.7 + - - +
526A ILE* 3.8 17.9 - - + +
582A TYR* 3.6 34.7 - - + -
585A ASP* 2.6 40.8 + - + +
587A GLU* 1.3 76.0 - - + +
589A VAL* 1.3 60.2 + - - +
591A ASN* 3.0 9.3 + - - +
592A LEU* 2.8 33.1 + - - +
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Residues in contact with VAL 589 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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579A LEU* 4.0 10.8 - - + -
582A TYR* 3.3 28.9 - - + +
583A SER* 3.6 21.5 - - - +
585A ASP 3.0 15.2 + - - +
586A ALA* 4.1 4.3 - - - +
588A LYS* 1.3 75.0 - - - +
590A ALA* 1.3 63.7 + - - +
592A LEU* 3.9 7.3 - - + +
593A LEU* 3.0 36.2 + - + +
623A VAL* 3.6 37.0 - - + -
627A HIS* 5.4 0.7 - - - +
632A VAL* 4.6 5.2 - - + -
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Residues in contact with ALA 590 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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586A ALA 3.1 18.1 + - - +
587A GLU* 3.7 7.0 - - - +
589A VAL* 1.3 80.3 - - - +
591A ASN* 1.3 59.5 + - - +
593A LEU* 3.7 5.6 + - - +
594A GLN* 3.0 27.8 + - - +
631A ASP* 4.2 33.4 - - + +
632A VAL* 4.6 2.9 - - - +
635A ALA* 4.2 9.6 - - + -
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Residues in contact with ASN 591 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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523A SER 4.4 2.9 - - - +
526A ILE* 3.6 16.2 - - + +
527A GLU* 3.6 38.7 + - - +
530A VAL* 3.6 17.5 - - + +
587A GLU 3.2 13.1 + - - +
588A LYS* 3.0 11.6 + - - +
590A ALA* 1.3 76.1 - - - +
592A LEU* 1.3 67.7 + - - +
594A GLN* 3.0 28.8 + - - +
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Residues in contact with LEU 592 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526A ILE* 4.0 32.5 - - + -
529A MET* 4.1 11.0 - - + -
575A LEU* 3.9 13.8 - - + +
578A LEU* 3.9 55.0 - - + +
579A LEU* 3.9 20.6 - - + -
582A TYR* 4.4 9.4 - - + -
588A LYS 2.8 23.5 + - - +
589A VAL* 3.9 1.6 - - + +
591A ASN* 1.3 74.3 - - - +
593A LEU* 1.4 53.4 + - - +
595A ILE* 2.8 43.8 + - + +
596A PRO* 3.9 1.7 - - - +
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Residues in contact with LEU 593 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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575A LEU* 5.2 2.9 - - + -
579A LEU* 4.0 28.3 - - + -
589A VAL* 3.0 40.0 + - + +
590A ALA 4.1 0.4 - - - +
591A ASN 3.2 0.6 - - - -
592A LEU* 1.4 73.9 - - - +
594A GLN* 1.3 61.5 + - - +
595A ILE 3.2 2.8 + - - -
596A PRO* 3.7 8.1 - - + +
597A GLN 5.4 0.5 + - - -
616A LEU* 4.9 2.5 - - + -
620A ILE* 4.1 18.2 - - + -
623A VAL* 4.8 1.6 - - + -
632A VAL 4.6 0.9 - - - +
635A ALA* 3.8 19.0 - - + +
636A CYS* 3.8 33.9 - - - +
638A LYS* 6.1 0.5 - - - +
639A THR* 3.4 32.8 + - + +
642A ILE* 5.8 2.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il